1
|
Wagner V, Kern F, Hahn O, Schaum N, Ludwig N, Fehlmann T, Engel A, Henn D, Rishik S, Isakova A, Tan M, Sit R, Neff N, Hart M, Meese E, Quake S, Wyss-Coray T, Keller A. Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues. Nat Biotechnol 2024; 42:109-118. [PMID: 37106037 DOI: 10.1038/s41587-023-01751-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.
Collapse
Affiliation(s)
- Viktoria Wagner
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Dominic Henn
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shusruto Rishik
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michelle Tan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rene Sit
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Norma Neff
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Martin Hart
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Saarland, Germany
| | - Steve Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, Saarbrücken, Germany.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany.
| |
Collapse
|
2
|
Engel A, Ludwig N, Grandke F, Wagner V, Kern F, Fehlmann T, Schmartz GP, Aparicio-Puerta E, Henn D, Walch-Rückheim B, Hannig M, Rupf S, Meese E, Laschke MW, Keller A. Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes. RNA Biol 2024; 21:31-44. [PMID: 38828710 PMCID: PMC11152102 DOI: 10.1080/15476286.2024.2361571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/05/2024] Open
Abstract
Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (five timepoints spanning 2 hours), we compare the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, mmu-miR-223-3p also exhibits an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single-cell sequencing of PBMCs reveals the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.
Collapse
Affiliation(s)
- Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg/Saar, Germany
- Center for Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Friederike Grandke
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Viktoria Wagner
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Georges P. Schmartz
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Dominic Henn
- Department of Plastic Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Barbara Walch-Rückheim
- Center of Human und Molecular Biology (ZHMB), Virology & Immunology, Saarland University, Homburg/Saar, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, Homburg/Saar, Germany
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, Homburg/Saar, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg/Saar, Germany
| | - Matthias W. Laschke
- Institute for Clinical and Experimental Surgery, Saarland University, Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarbrücken, Germany
| |
Collapse
|
3
|
Rego N, Libisch MG, Rovira C, Tosar JP, Robello C. Comparative microRNA profiling of Trypanosoma cruzi infected human cells. Front Cell Infect Microbiol 2023; 13:1187375. [PMID: 37424776 PMCID: PMC10322668 DOI: 10.3389/fcimb.2023.1187375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Trypanosoma cruzi, the causative agent of Chagas disease, can infect almost any nucleated cell in the mammalian host. Although previous studies have described the transcriptomic changes that occur in host cells during parasite infection, the understanding of the role of post-transcriptional regulation in this process is limited. MicroRNAs, a class of short non-coding RNAs, are key players in regulating gene expression at the post-transcriptional level, and their involvement in the host-T. cruzi interplay is a growing area of research. However, to our knowledge, there are no comparative studies on the microRNA changes that occur in different cell types in response to T. cruzi infection. Methods and results Here we investigated microRNA changes in epithelial cells, cardiomyocytes and macrophages infected with T. cruzi for 24 hours, using small RNA sequencing followed by careful bioinformatics analysis. We show that, although microRNAs are highly cell type-specific, a signature of three microRNAs -miR-146a, miR-708 and miR-1246, emerges as consistently responsive to T. cruzi infection across representative human cell types. T. cruzi lacks canonical microRNA-induced silencing mechanisms and we confirm that it does not produce any small RNA that mimics known host microRNAs. We found that macrophages show a broad response to parasite infection, while microRNA changes in epithelial and cardiomyocytes are modest. Complementary data indicated that cardiomyocyte response may be greater at early time points of infection. Conclusions Our findings emphasize the significance of considering microRNA changes at the cellular level and complement previous studies conducted at higher organizational levels, such as heart samples. While miR-146a has been previously implicated in T. cruzi infection, similarly to its involvement in many other immunological responses, miR-1246 and miR-708 are demonstrated here for the first time. Given their expression in multiple cell types, we anticipate our work as a starting point for future investigations into their role in the post-transcriptional regulation of T. cruzi infected cells and their potential as biomarkers for Chagas disease.
Collapse
Affiliation(s)
- Natalia Rego
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - María Gabriela Libisch
- Laboratorio de Interacciones Hospedero Patógeno/UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Rovira
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Juan Pablo Tosar
- Laboratorio de Genómica Funcional, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Unidad de Bioquímica Analítica, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero Patógeno/UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
4
|
Aparicio-Puerta E, Hirsch P, Schmartz GP, Kern F, Fehlmann T, Keller A. miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations. Nucleic Acids Res 2023:7161530. [PMID: 37177999 DOI: 10.1093/nar/gkad392] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/21/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/.
Collapse
Affiliation(s)
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| |
Collapse
|
5
|
Jenike AE, Jenike KM, Peterson KJ, Fromm B, Halushka MK. Direct observation of the evolution of cell-type-specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells. Evol Dev 2023; 25:226-239. [PMID: 37157156 PMCID: PMC10302300 DOI: 10.1111/ede.12438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/22/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
The evolution of specialized cell-types is a long-standing interest of biologists, but given the deep time-scales very difficult to reconstruct or observe. microRNAs have been linked to the evolution of cellular complexity and may inform on specialization. The endothelium is a vertebrate-specific specialization of the circulatory system that enabled a critical new level of vasoregulation. The evolutionary origin of these endothelial cells is unclear. We hypothesized that Mir-126, an endothelial cell-specific microRNA may be informative. We here reconstruct the evolutionary history of Mir-126. Mir-126 likely appeared in the last common ancestor of vertebrates and tunicates, which was a species without an endothelium, within an intron of the evolutionary much older EGF Like Domain Multiple (Egfl) locus. Mir-126 has a complex evolutionary history due to duplications and losses of both the host gene and the microRNA. Taking advantage of the strong evolutionary conservation of the microRNA among Olfactores, and using RNA in situ hybridization, we localized Mir-126 in the tunicate Ciona robusta. We found exclusive expression of the mature Mir-126 in granular amebocytes, supporting a long-proposed scenario that endothelial cells arose from hemoblasts, a type of proto-endothelial amoebocyte found throughout invertebrates. This observed change of expression of Mir-126 from proto-endothelial amoebocytes in the tunicate to endothelial cells in vertebrates is the first direct observation of the evolution of a cell-type in relation to microRNA expression indicating that microRNAs can be a prerequisite of cell-type evolution.
Collapse
Affiliation(s)
- Ana E. Jenike
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Katharine M. Jenike
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover NH, USA
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, 9006 Tromsø, Norway
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| |
Collapse
|
6
|
Aparicio-Puerta E, Hirsch P, Schmartz GP, Fehlmann T, Keller V, Engel A, Kern F, Hackenberg M, Keller A. isomiRdb: microRNA expression at isoform resolution. Nucleic Acids Res 2022; 51:D179-D185. [PMID: 36243964 PMCID: PMC9825445 DOI: 10.1093/nar/gkac884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023] Open
Abstract
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.
Collapse
Affiliation(s)
| | | | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Rejuvenome, Astera Institute, Berkeley, CA 94705, USA
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Department for Internal Medicine II, Saarland University Hospital, 66421 Homburg, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, Universidad de Granada, 18071 Granada, Spain
| | - Andreas Keller
- To whom correspondence should be addressed. Tel: +49 681 30268611; Fax: +49 681 30268610;
| |
Collapse
|